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- EMDB-10427: Structure of the five-fold capsomer of the dArc2 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-10427
TitleStructure of the five-fold capsomer of the dArc2 capsid
Map datadArc2 five-fold capsomer
Sample
  • Cell: dArc2 Capsids
    • Protein or peptide: Activity-regulated cytoskeleton associated protein 2
KeywordsdArc / Gag / Virus / VLP / VIRUS LIKE PARTICLE
Function / homologyTy3 transposon capsid-like protein / Ty3 transposon capsid-like protein / virus-like capsid / extracellular vesicle / structural molecule activity / RNA binding / identical protein binding / membrane / Activity-regulated cytoskeleton associated protein 2
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsErlendsson S / Morado DR
Funding support Denmark, United States, United Kingdom, 3 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0030788 Denmark
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-MH112766 United States
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Nat Neurosci / Year: 2020
Title: Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins.
Authors: Simon Erlendsson / Dustin R Morado / Harrison B Cullen / Cedric Feschotte / Jason D Shepherd / John A G Briggs /
Abstract: Arc, a neuronal gene that is critical for synaptic plasticity, originated through the domestication of retrotransposon Gag genes and mediates intercellular messenger RNA transfer. We report high- ...Arc, a neuronal gene that is critical for synaptic plasticity, originated through the domestication of retrotransposon Gag genes and mediates intercellular messenger RNA transfer. We report high-resolution structures of retrovirus-like capsids formed by Drosophila dArc1 and dArc2 that have surface spikes and putative internal RNA-binding domains. These data demonstrate that virus-like capsid-forming properties of Arc are evolutionarily conserved and provide a structural basis for understanding their function in intercellular communication.
History
DepositionOct 30, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseJan 1, 2020-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6tat
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tat
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10427.png

Downloads & links

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Map

FileDownload / File: emd_10427.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdArc2 five-fold capsomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 148 pix.
= 205.424 Å		1.39 Å/pix.
x 148 pix.
= 205.424 Å		1.39 Å/pix.
x 148 pix.
= 205.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.388 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.007047234 - 0.44123968
Average (Standard dev.)0.0015141699 (±0.013864755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions148148148
Spacing148148148
CellA=B=C: 205.424 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3881.3881.388
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z205.424205.424205.424
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS148148148
D min/max/mean-0.0070.4410.002

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Supplemental data

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Additional map: dArc2 five-fold capsomer unsharpened

Fileemd_10427_additional.map
AnnotationdArc2 five-fold capsomer unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dArc2 Capsids

EntireName: dArc2 Capsids
Components
  • Cell: dArc2 Capsids
    • Protein or peptide: Activity-regulated cytoskeleton associated protein 2

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Supramolecule #1: dArc2 Capsids

SupramoleculeName: dArc2 Capsids / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The five-fold dArc2 capsomer map is generated by symmetry expansion, sub-boxing and local refinement.
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Activity-regulated cytoskeleton associated protein 2

MacromoleculeName: Activity-regulated cytoskeleton associated protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 22.656734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQMSDEQFR IFIETIKSLG PIKEEPPSKG SFSNCTVRFS GQRDHDAVDE FINAVETYKE VEGISDKDAL KGLPLLFKSI AVVWWKGVR RDAKTWSDAL QLLRDHFSPT KPSYQIYMEI FETKQSYDEV IDSFICKQRA LLAKLPEGRH DEETELDFIY G LMQPKYRE ...String:
MTQMSDEQFR IFIETIKSLG PIKEEPPSKG SFSNCTVRFS GQRDHDAVDE FINAVETYKE VEGISDKDAL KGLPLLFKSI AVVWWKGVR RDAKTWSDAL QLLRDHFSPT KPSYQIYMEI FETKQSYDEV IDSFICKQRA LLAKLPEGRH DEETELDFIY G LMQPKYRE SIPRHEVKTF RELLDRGRTV ERTRH

UniProtKB: Activity-regulated cytoskeleton associated protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMC4H11NO3Tris
1.0 mMC4H10O2S2DTT
50.0 uMZnCl2zinc cloride
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsdArc2 capsids

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-75 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 21348
Details: From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units ...Details: From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units for dArc2, centered at the five-fold capsomeres. We extracted individual capsomeres using a box size of 148 pixels. For the five-fold capsomeres we removed the redundant five-fold symmetrized capsomeres leaving 21,348 particles.
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 21348
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

6gse


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6tat:
Structure of the five-fold capsomer of the dArc2 capsid

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